Organization and Format

Editorial Style

The editorial style of ASM journals conforms to the ASM Style Manual for Journals (American Society for Microbiology, 2017, in-house document [you may find the ASM Word List helpful]) and How To Write and Publish a Scientific Paper, 7th ed. (Greenwood, Santa Barbara, CA, 2011), as interpreted and modified by the editors and the ASM Journals Department.

The editors and the Journals Department reserve the privilege of editing manuscripts to conform with the stylistic conventions set forth in the aforesaid publications and in these Instructions.

On receipt at ASM, an accepted manuscript undergoes an automated preediting, cleanup, and tagging process specific to the particular article type. To optimize this process, manuscripts must be supplied in the correct format and with the appropriate sections and headings.

Type every portion of the manuscript double-spaced (a minimum of 6 mm between lines), including figure legends, table footnotes, and references, and number all pages in sequence, including the abstract, figure legends, and tables. Place the last two items after the References section. Manuscript pages should have line numbers; manuscripts without line numbers may be editorially rejected by the editor, with a suggestion of resubmission after line numbers are added. The font size should be no smaller than 12 points. It is recommended that the following sets of characters be easily distinguishable in the manuscript: the numeral zero (0) and the letter “oh” (O); the numeral one (1), the letter “el” (l), and the letter “eye” (I); and a multiplication sign and the letter “ex” (x). Do not create symbols as graphics or use special fonts that are external to your word processing program; use the “insert symbol” function. Set the page size to 8.5 by 11 inches (ca. 21.6 by 28 cm). Italicize any words that should appear in italics, and indicate paragraph lead-ins in boldface type. Authors who are unsure of proper English usage should have their manuscripts checked by someone proficient in the English language.

Manuscripts may be editorially rejected, without review, on the basis of poor English or lack of conformity to the standards set forth in these Instructions.

Article Word Count

mSphere® article word counts are based on the article type. Research Articles and Resource Reports should be approximately 5,000 words. Minireviews should be approximately 3,000 words maximum (with up to two figures or tables). Opinions/Hypotheses should be approximately 2,500 words maximum. Perspectives should be approximately 2,000 words maximum. Observations should be approximately 1,200 words maximum. Commentaries should be approximately 1,000 words maximum. Letters to the Editor and Replies should each be approximately 500 words maximum. Word counts do not include Materials and Methods, References, tables, or figure legends.

Authors will be asked to shorten overlong papers.

Supplemental Material

Authors should use discretion regarding supplemental material. Data that directly support the main conclusions of the manuscript should be part of the body of the manuscript to the greatest extent possible: both reviewers and readers prefer this practice.

Large or complex data sets or results that cannot readily be displayed in printed form because of space or technical limitations, such as data from gene expression, genomic, metagenomic, structural, proteomic, or video imaging analyses, can be included as supplemental material. In such cases, the manuscript submitted for review should include a distillation of the results so that the principal conclusions are fully supported without referral to the supplemental material.

Supplemental material can be posted by mSphere or, if authors prefer, can be submitted by the authors for posting by a third-party service such as Dryad, figshare, or a similar repository. In the latter case, the assigned accession number(s) must be included in the manuscript submitted for review.

Supplemental material will be peer reviewed along with the manuscript and, if intended for posting by mSphere, must be uploaded to the eJournalPress (eJP) peer review system at initial manuscript submission. For initial submission, this material may be uploaded as a single PDF. At the modification stage, however, each item in the supplemental material must be submitted as a separate file; e.g., multiple figures and/or tables should not be zipped together or combined in a single PDF. Legends should not be included in the supplemental files; rather, they should appear at the end of the main manuscript text (see next paragraph). ASM will post no more than 10 individual supplemental items. The maximum size permitted for an individual file is 3 MB (20 MB for movie or Excel data set files).

To ensure broad access, we ask that supplemental files be submitted in the following standard formats.

At the end of the manuscript text file, include a legend for each item in the supplemental material. If it is necessary to cite references that are relevant only to these supplemental legends, use the style described for “Citations in abstracts”; do not include these references in the References section of the manuscript. Supplemental material should be numbered with an “S” (e.g., Movie S1, Fig. S1, Fig. S2, etc.), and each item should be cited at least once in the text.

Supplemental material posted by mSphere will not be edited by the ASM Journals staff, and proofs will not be made available. Supplemental material posted by mSphere will always remain associated with the article and is not subject to any modifications after publication.

Material that has been published previously (in print or online) is not acceptable for posting as supplemental material. Instead, the appropriate reference(s) to the original publication should be made in the manuscript text.

Supplemental material is covered by the mSphere Author Warranty and Provisional License to Publish; copyright for supplemental material remains with the author. If you are not the copyright owner, you must provide to ASM signed permission from the owner that allows ASM to post the material as a supplement to your article. You are responsible for including in the supplemental material any copyright notices required by the owner.

For information about supplemental material posting fees, see “Publication Fees.”

Research Articles

Research Articles are limited to 5,000 words, not including the References section and figure legends, and should make fundamental contributions to our understanding of any area of microbiology or allied fields. These articles should include the elements described in this section.

Title, running title, and byline. Each manuscript should present the results of an independent, cohesive study; thus, numbered series titles are not allowed. Avoid the main title/subtitle arrangement, complete sentences, and unnecessary articles. Indicate the specific organisms under study in the title or abstract as appropriate. On the title page, include the title, the running title (not to exceed 54 characters and spaces), the name of each author, the address(es) of the institution(s) at which the work was performed, each author’s affiliation, and a footnote indicating the present address of any author no longer at the institution where the work was performed. Place a number sign (#) in the byline after the name of the author to whom inquiries regarding the paper should be addressed (see “Correspondent footnote”).

Also include on the title page the word count for the abstract and the word count for the text (excluding the references, table footnotes, and figure legends).

Correspondent footnote. A single e-mail address for the corresponding author should be included on the title page of the manuscript. This information will be published with the article to facilitate communication, and the e-mail address will be used to notify the corresponding author of the availability of proofs and, later, of the PDF file of the published article.

Two-part abstract. Research Articles have structured abstracts consisting of two sections with their own headings: “Abstract” and “Importance.” Because the structured abstract will be published separately by abstracting services, it must be complete and understandable without reference to the text. Please refer to the sample structured abstract for guidance.

The Abstract section should be no more than 250 words and should concisely summarize the basic content of the paper without presenting extensive experimental details.

The Importance section should be no more than 150 words and should provide a nontechnical explanation of the significance of the study to the field. Avoid abbreviations and references, and indicate the specific organism under study. When it is essential to include a reference, use the format shown under “References” below (see the “Citations in abstracts” section).

Introduction. The introduction should supply sufficient background information to allow the reader to understand and evaluate the results of the present study without referring to previous publications on the topic. The introduction should also provide the hypothesis that was addressed or the rationale for the present study. Choose references carefully to provide the most salient background rather than an exhaustive review of the topic.

Results. In the Results section, include the rationale or design of the experiments as well as the results; reserve extensive interpretation of the results for the Discussion section. Present the results as concisely as possible in one or more of the following: text, table(s), or figure(s). Data in tables (e.g., cpm of radioactivity) should not contain more significant figures than the precision of the measurement allows. Number figures and tables in the order in which they are cited in the text, and be sure to cite all figures and tables.

References to "data not shown" should generally be limited to negative results. It is at the editor’s discretion whether an assertion supported by "data not shown" is important enough that the data need to be presented.

Discussion. The Discussion section should provide an interpretation of the results in relation to previously published work and to the experimental system at hand and should not contain extensive repetition of the Results section or reiteration of the introduction. In short papers, the Results and Discussion sections may be combined.

Materials and Methods. The Materials and Methods section should include sufficient technical information to allow the experiments to be repeated. When centrifugation conditions are critical, give enough information to enable another investigator to repeat the procedure: make of centrifuge, model of rotor, temperature, time at maximum speed, and centrifugal force (× g rather than revolutions per minute). For commonly used materials and methods (e.g., media and protein concentration determinations), a simple reference is sufficient. If several alternative methods are commonly used, it is helpful to identify the method briefly as well as to cite the reference. For example, it is preferable to state “cells were broken by ultrasonic treatment as previously described (9)” rather than to state “cells were broken as previously described (9).” This allows the reader to assess the method without constant reference to previous publications. Describe new methods completely and give sources of unusual chemicals, equipment, or microbial strains. When large numbers of microbial strains or mutants are used in a study, include tables identifying the immediate sources (i.e., sources from whom the strains were obtained) and properties of the strains, mutants, bacteriophages, and plasmids, etc.

A method or strain, etc., used in only one of several experiments reported in the paper may be described in the Results section or very briefly (one or two sentences) in a table footnote or figure legend. It is expected that the sources from whom the strains were obtained will be identified.

As noted above, a paragraph dedicated to new accession numbers for nucleotide and amino acid sequences, microarray data, protein structures, gene expression data, and MycoBank data should appear at the end of Materials and Methods with the paragraph lead-in "Accession number(s)." Please also provide references (with URLs or DOIs) for the accession numbers

Acknowledgments. Statements regarding sources of direct financial support (e.g., grants, fellowships, and scholarships, etc.) should appear in the Acknowledgments. A funding statement indicating what role, if any, the funding agency had in your study (for example, “The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.”) may be included. Funding agencies may have specific wording requirements, and compliance with such requirements is the responsibility of the author. In cases in which research is not funded by any specific project grant, funders need not be listed, and the following statement may be used: “This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.” Statements regarding indirect financial support (e.g., commercial affiliations, consultancies, stock or equity interests, and patent-licensing arrangements) are also allowed. It is the responsibility of authors to provide a general statement disclosing financial or other relationships that are relevant to the study. (See Conflict of Interest.)

Recognition of personal assistance should be given as a separate paragraph, as should any statements disclaiming endorsement or approval of the views reflected in the paper or of a product mentioned therein.

In addition to acknowledging sources of financial support in the manuscript, authors should list any sources of funding in response to the Funding Sources question on the online submission form, providing relevant grant numbers where possible, and the authors associated with the specific funding sources. In the event that your submission is accepted, the funding source information provided in the submission form may be published, so please ensure that all information is entered accurately and completely. (It will be assumed that the absence of any information in the Funding Sources fields is a statement by the authors that no support was received.)

References. In the reference list, references are numbered in the order in which they are cited in the article (citation-sequence reference system). In the text, references are cited parenthetically by number in sequential order. Data that are not published or not peer reviewed are simply cited parenthetically in the text (see section ii below).

(i) References listed in the References section. The following types of references must be listed in the References section:

Provide the names of all the authors and/or editors for each reference; long bylines should not be abbreviated with “et al.” All listed references must be cited in the text. Abbreviate journal names according to the PubMed Journals Database (National Library of Medicine, National Institutes of Health), the primary source for ASM style. Do not use periods with abbreviated words. The EndNote output style for ASM Journals’ current reference style can be found here; click “Open” and then “Download and Install” to save it to your EndNote Styles folder (it should replace any earlier output styles for ASM journals [all ASM journals use the same reference style]). Note that DOIs are not needed for most references, but see the exception for reference 17 below. ASM copy editors will automatically insert DOIs on all references in the CrossRef and PubMed databases during copyediting. URLs for government reports and other references not indexed in these databases should be provided if desired; URLs or DOIs for citations of database accession numbers and code/software should be provided by you.

Falagas ME, Kasiakou SK. 2006. Use of international units when dosing colistin will help decrease confusion related to various formulations of the drug around the world. Antimicrob Agents Chemother 50:2274–2275. (Letter.) {“Letter” or “Letter to the editor” is allowed but not required at the end of such an entry.}

*A reference to an in-press ASM publication should state the control number (e.g., mSphere00001-17) if it is a journal article or the name of the publication if it is a book.

In some online journal articles, posting or revision dates may serve as the year of publication, and a DOI (preferred) or URL is required for articles with nontraditional page numbers or electronic article identifiers.

Other journals may use different styles for their publish ahead-of-print manuscripts, but citation entries must include the following information: author name(s), posting date, title, journal title, and volume and page numbers and/or DOI. The following is an example:

To encourage data sharing and reuse, ASM recommends reporting data sets and/or code both in a dedicated “Data availability” paragraph and in References. The components of a complete data citation include the following:

Responsible party (senior author, collector, agency),

Publication year,

Complete name of a data set, including the name of the database or repository and its URL, or the name of the analysis software (if appropriate), including the version and project,

Manuscript submissions that have appeared in preprint archives should cite the preprint in References, and the fact that a paper has appeared online before should be mentioned parenthetically at the end of the introductory section: (This article was submitted to an online preprint archive [1].) The reference should take the form noted above in reference 18.

(ii) References cited in the text. References that should be cited in the text include the following:

Unpublished data

Manuscripts submitted for publication

Unpublished conference presentations (e.g., a report or poster that has not appeared in published conference proceedings)

Personal communications

Patent applications and patents pending

Websites

These references should be made parenthetically in the text as follows:

URLs for companies that produce any of the products mentioned in your study or for products being sold may not be included in the article. However, company URLs that permit access to scientific data related to the study or to shareware used in the study are permitted.

(iii) Citations in abstracts. Since the abstract must be able to stand apart from the article, references cited in it should be clear without recourse to the References section. Use an abbreviated form of citation, omitting the article title, as follows.

When necessary, this style should also be used for references cited in legends for supplemental material and in Addenda in Proof.

(iv) References related to supplemental material. If references must be cited in the supplemental material, list them in a separate References section within the supplemental material and cite them by those numbers; do not simply include citations of numbers from the reference list of the associated article. If the same reference(s) is to be cited in both the article itself and the supplemental material, then that reference would be listed in both References sections.

Observations

Observations are short descriptions (maximum 1,200 words with a maximum of 2 figures and 25 references) of research results of exceptional importance and unusual interest to the broad microbiology community, e.g., reports of a new type of organism, a new organelle, a new association of microbes and disease, etc.

The body of an Observation may have paragraph lead-ins. As with Research Articles, authors should include an abstract of 250 words or fewer as well as an Importance section of 150 words or fewer, providing a nontechnical explanation of why the work was undertaken.

As noted above under "Data and Materials," a paragraph dedicated to new accession numbers for nucleotide and amino acid sequences, microarray data, protein structures, gene expression data, and MycoBank data should appear at the end of the text with the paragraph lead-in "Accession number(s)."

Minireviews

Minireviews are invited, brief (maximum 3,000 words, with a maximum of 2 figures and 25 references) summaries of important developments in microbiology research. They must be based on published articles and may address any subject within the scope of the journal.

Minireviews must have abstracts. Limit the abstract to 250 words or fewer. The body of the Minireview may have section headings and/or paragraph lead-ins.

Opinions/Hypotheses

Opinions/Hypotheses are short articles (maximum 2,500 words with a maximum of 25 references) that present original and well-developed insights without complete supporting data. Although microbiology and allied fields are primarily experimental sciences, this article type places equal importance on new thought that is formulated in a manner that summarizes a problem, provides a new synthesis, and/or is suitable for subsequent experimental testing.

In this category, the journal provides a highly visible venue for the publication of ideas that have the potential to move fields and to challenge the status quo.

Authors should provide an abstract of 150 words or fewer. The body of an Opinion/Hypothesis article may have section headings and/or paragraph lead-ins.

Resource Reports

Resource Reports (5,000 word limit) describe major technical advances and/or major informational databases that would be of interest in microbiology or allied fields. The manuscripts should include detailed methods and illustration of proof of principle so that the new methodology can be replicated and/or utilized by others. Resource reports follow the same formatting guidelines as Research Articles.

Commentaries

Commentaries are short invited articles (maximum 1,000 words) that discuss mSphere papers or issues of special interest. These are solicited by editors from reviewers or experts in the field.

Authors should provide an abstract of 150 words or fewer. The body of a Commentary may have section headings and/or paragraph lead-ins.

Perspectives

Perspectives are brief reviews (maximum 2,000 words) that offer a succinct overview of a specific topic with an emphasis on opinion and synthesis.

Authors should provide an abstract of 150 words or fewer. The body of a Perspectives article may have section headings and/or paragraph lead-ins.

Editorials

Editorials (maximum 500 words) communicated by members of the mSphere Board of Editors address issues of science, politics, or policy.

Editorials should include an abstract of 150 words or fewer.

Letters to the Editor

Letters to the Editor are intended for comments on articles published in the journal and must cite published references to support the writer’s argument. Letters may be no more than 500 words long and must be typed double-spaced.

All Letters to the Editor must be submitted electronically. The cover letter should refer to the article in question by its title and the last name of the first author. In addition, the volume and issue and/or DOI should be indicated. Letters to the Editor do not have abstracts. The Letter must have a distinct title, which must appear on the manuscript and on the submission form. Figures and tables should be kept to a minimum.

The Letter will be sent to the editor who handled the article in question. If the editor believes that publication is warranted, he/she will solicit a reply from the corresponding author of the article and make a recommendation to the editor in chief. Final approval for publication rests with the editor in chief.

Please note that some indexing/abstracting services do not include Letters to the Editor in their databases.